Yes you can, it's just that you have to match the Ohm ratings of the stock system with the new components. Most aftermarket products operate on a 4 Ohm system, where are some factory systems run off a 1 Ohm system. This only applies if you try and add speakers on the existing system.
If you plan on running an amp with subs, you can use an adapter like this one that will let you convert the 9-pin port in the back of the radio to allow you to run an amp via RCA cables. Read more.